Identify mobile genetic elements present in genomic assemblies
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
FASTA file containing contigs/scaffolds/chromosomes
*.{fasta,fna,fa}
genomad_db{:bash}
:directory
Directory pointing to geNomad database
aggregated_classification{:bash}
*_aggregated_classification/*_aggregated_classification.tsv{:bash}
Combined classification scores for each contig/scaffold/chromosome
*_aggregated_classification.tsv
marker_classification{:bash}
*_marker_classification/*_marker_classification.tsv{:bash}
Marker-based classification scores when —disable-nn-classification is used
*_marker_classification.tsv
taxonomy{:bash}
*_annotate/*_taxonomy.tsv{:bash}
Detailed output of geNomad’s marker gene taxonomy analysis
*_taxonomy.tsv
provirus{:bash}
*_find_proviruses/*_provirus.tsv{:bash}
Detailed output of each provirus identified by geNomad’s find_proviruses module
*_provirus.tsv
compositions{:bash}
*_score_calibration/*_compositions.tsv{:bash}
OPTIONAL - Predicted sample composition when --enable-score-calibration is used
--enable-score-calibration
*_compositions.tsv
calibrated_classification{:bash}
*_score_calibration/*_calibrated_aggregated_classification.tsv{:bash}
OPTIONAL - Classification scores that have been adjusted based on sample composition when --enable-score-calibration is used`
*_calibrated_aggregated_classification.tsv
plasmid_fasta{:bash}
*_summary/*_plasmid.fna.gz{:bash}
FASTA file containing predicted plasmid sequences
*_plasmid.fna
plasmid_genes{:bash}
*_summary/*_plasmid_genes.tsv{:bash}
TSV file containing predicted plasmid genes and their annotations
*_plasmid_genes.tsv
plasmid_proteins{:bash}
*_summary/*_plasmid_proteins.faa.gz{:bash}
FASTA file containing predicted plasmid protein sequences
*_plasmid_proteins.faa
plasmid_summary{:bash}
*_summary/*_plasmid_summary.tsv{:bash}
TSV file containing a summary of geNomad’s plasmid predictions
*_plasmid_summary.tsv
virus_fasta{:bash}
*_summary/*_virus.fna.gz{:bash}
FASTA file containing predicted virus sequences
*_virus.fna
virus_genes{:bash}
*_summary/*_virus_genes.tsv{:bash}
TSV file containing predicted virus genes and their annotations
*_virus_genes.tsv
virus_proteins{:bash}
*_summary/*_virus_proteins.faa.gz{:bash}
FASTA file containing predicted virus protein sequences
*_virus_proteins.faa
virus_summary{:bash}
*_summary/*_virus_summary.tsv{:bash}
TSV file containing a summary of geNomad’s virus predictions
*_virus_summary.tsv
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Identification of mobile genetic elements
